Contacts of the helix formed by residues 392 - 414 (chain A) in PDB entry 5E8T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ASP* 4.7 12.9 + - - -
365A ILE* 4.5 2.2 - - - -
389A ASN* 3.2 30.9 + - + +
391A LYS* 1.4 76.1 - - - +
393A PHE* 1.4 68.7 + - - +
394A GLU* 3.7 21.9 - - + +
395A SER* 3.0 38.9 + - - +
396A PHE* 3.9 5.4 + - - -
398A ARG* 3.9 17.8 + - - -
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Residues in contact with PHE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 3.5 33.9 - - + -
329A ILE 3.6 2.2 - - - -
330A ALA* 3.5 31.9 - - + -
356A VAL* 3.6 27.6 - - + -
358A HIS* 3.4 51.8 - + + +
363A ASP* 4.3 5.2 + - - +
365A ILE* 4.1 23.4 - - + +
391A LYS 3.8 4.6 + - - -
392A HIS* 1.4 73.4 + - - +
394A GLU* 1.3 65.4 + - - +
396A PHE* 2.9 18.5 + + - +
397A LYS* 3.4 30.7 + - + -
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A HIS* 3.3 24.2 + - + +
393A PHE* 1.3 78.9 - - - +
395A SER* 1.3 55.5 - - - +
397A LYS* 2.9 47.0 + - - +
398A ARG* 3.0 63.9 + - - +
484A THR* 5.1 9.9 - - - +
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Residues in contact with SER 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 4.4 3.0 - - - +
388A ILE* 3.7 22.4 - - - +
389A ASN* 3.5 22.1 + - - +
392A HIS* 3.0 34.8 + - - +
394A GLU* 1.3 76.6 - - - +
396A PHE* 1.4 55.5 + - - +
398A ARG* 3.4 14.4 + - - +
399A ALA* 3.1 26.9 + - - +
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Residues in contact with PHE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA* 3.5 22.4 - - + -
332A ARG* 3.6 32.3 - - + +
356A VAL* 4.1 11.7 - - + -
365A ILE* 3.8 17.5 - - + -
369A PRO* 3.7 24.5 - - + -
370A ASN 5.8 0.2 - - - -
383A VAL* 6.3 0.7 - - + -
388A ILE* 4.4 13.5 - - + -
389A ASN 5.0 0.4 - - - -
390A MET* 3.4 50.9 - - + -
392A HIS 4.0 10.1 - - - -
393A PHE* 2.9 10.2 + - + +
395A SER* 1.4 74.6 - - - +
397A LYS* 1.4 64.6 + - - +
399A ALA* 3.3 9.0 + - + +
400A ASP* 3.1 26.5 + - - +
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Residues in contact with LYS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A HIS* 3.4 57.7 + - + +
328A ALA* 5.3 0.2 - - + -
330A ALA* 4.1 1.1 - - + +
393A PHE* 3.4 36.9 + - + +
394A GLU* 2.9 44.6 + - - +
396A PHE* 1.4 76.2 - - - +
398A ARG* 1.3 62.4 + - + +
400A ASP* 3.2 6.1 + - - +
401A ILE* 3.2 26.6 + - + +
484A THR* 5.9 6.2 - - - +
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 4.7 0.9 - - - +
392A HIS* 3.9 23.4 + - - -
394A GLU* 3.0 49.7 + - + +
395A SER* 3.6 11.0 + - - +
396A PHE 3.3 0.2 - - - -
397A LYS* 1.3 73.7 - - - +
399A ALA* 1.4 64.7 + - - +
401A ILE* 3.2 19.3 + - + +
402A TYR 3.3 5.5 + - - -
479A GLY* 3.4 34.5 - - - +
480A ALA* 3.7 32.9 + - - +
482A ARG* 2.9 20.1 + - + +
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 6.5 0.9 - - - -
378A TYR 5.1 0.7 - - - +
380A ALA* 3.9 19.8 + - + +
382A GLU* 3.9 3.8 - - - +
383A VAL* 4.3 15.9 - - + -
388A ILE* 4.6 2.9 - - + -
395A SER 3.1 14.0 + - - +
396A PHE* 3.3 12.3 + - + +
398A ARG* 1.4 75.7 - - - +
400A ASP* 1.4 63.6 + - - +
402A TYR* 3.4 6.1 + - - +
403A ALA* 3.3 19.4 + - - +
482A ARG* 3.8 8.5 - - - +
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 3.9 11.2 - - + +
317A HIS* 2.8 26.8 + - + +
330A ALA* 3.4 2.6 - - - +
331A HIS* 2.7 32.4 + - - +
332A ARG* 3.0 28.6 + - - -
333A ASP 4.6 0.5 + - - -
334A LEU* 3.8 8.9 + - + +
396A PHE 3.1 15.0 + - - +
397A LYS 3.2 8.7 + - - +
399A ALA* 1.4 77.7 - - - +
401A ILE* 1.4 57.0 + - - +
403A ALA* 3.2 9.1 + - - +
404A MET* 2.8 28.2 + - - +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LEU* 3.8 12.6 - - + -
317A HIS* 4.3 4.3 - - + +
397A LYS* 3.2 16.5 + - + +
398A ARG* 3.2 11.8 + - - +
400A ASP* 1.4 71.6 - - - +
402A TYR* 1.3 66.9 + - - +
404A MET* 3.2 12.0 + - + +
405A GLY 2.9 19.1 + - - -
474A CYS* 3.5 28.1 - - + +
482A ARG* 4.1 11.0 - - + -
483A LEU 3.3 24.2 - - - +
484A THR* 3.9 2.7 - - - -
485A ALA* 3.4 42.0 - - + +
488A ILE* 4.2 2.7 - - + -
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Residues in contact with TYR 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ARG 4.8 0.5 + - - -
378A TYR 3.6 13.2 - - - -
379A MET 3.4 20.5 + - - -
380A ALA* 3.4 17.0 - - + -
381A PRO* 3.8 19.1 - - + -
398A ARG 3.3 3.4 + - - -
399A ALA 3.5 7.6 - - - +
400A ASP 3.3 0.2 - - - -
401A ILE* 1.3 78.2 - - - +
403A ALA* 1.4 64.0 + - - +
405A GLY* 3.1 11.8 + - - -
406A LEU* 3.2 26.0 + - + +
428A TYR* 2.7 33.8 + - - -
445A VAL* 3.7 11.1 - - - +
451A ARG* 3.9 18.6 - - - -
474A CYS 3.3 21.1 + - - +
475A TRP* 3.6 28.7 + + - -
482A ARG* 3.9 18.2 - - - +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 3.5 32.5 - - + +
378A TYR* 3.8 20.1 - - + +
399A ALA 3.3 7.4 + - - +
400A ASP* 3.2 9.9 + - - +
402A TYR* 1.4 84.6 - - - +
404A MET* 1.3 61.3 + - - +
406A LEU* 3.1 11.6 + - - +
407A VAL* 3.0 25.2 + - - +
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Residues in contact with MET 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A THR* 3.9 20.2 - - + -
310A ALA* 3.8 25.1 - - + -
313A LEU* 3.8 23.8 - - + -
334A LEU* 3.8 13.1 - - + +
400A ASP 2.8 17.1 + - - +
401A ILE* 3.2 10.5 + - + +
403A ALA* 1.3 71.9 - - - +
405A GLY* 1.3 56.4 + - - +
407A VAL* 3.2 6.6 + - + +
408A PHE* 2.9 46.1 + - + -
474A CYS* 5.1 1.1 - - - -
485A ALA* 4.9 2.9 - - - -
488A ILE* 3.6 43.7 - - + -
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE 2.9 11.5 + - - -
402A TYR 3.1 5.1 + - - -
404A MET* 1.3 75.0 - - - +
406A LEU* 1.4 62.1 + - - +
408A PHE* 3.2 10.5 + - - +
409A TRP 3.1 17.8 + - - -
471A MET* 3.7 5.5 - - - +
474A CYS* 3.8 20.1 - - - +
475A TRP* 3.4 22.6 - - - -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ARG 3.9 7.9 - - - +
378A TYR* 3.8 30.7 - - + -
402A TYR* 3.2 38.7 + - + +
403A ALA* 3.1 7.7 + - - +
405A GLY* 1.4 75.5 - - - +
407A VAL* 1.3 62.5 + - - +
409A TRP* 3.2 8.6 + - - +
410A GLU* 3.2 24.3 + - - +
427A PRO* 4.0 14.0 - - + +
428A TYR* 3.9 13.7 - - + +
452A PRO* 3.6 32.1 - - + -
475A TRP* 3.3 20.1 - - + +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU* 3.6 30.1 - - + -
309A THR* 4.9 3.6 - - + -
334A LEU* 4.9 2.0 - - + -
335A LYS* 3.9 14.4 - - - +
336A SER* 3.8 26.0 - - - +
339A ILE* 3.8 16.2 - - + -
378A TYR* 4.0 5.2 - - + -
403A ALA 3.0 15.9 + - - +
404A MET* 3.2 11.6 + - + +
406A LEU* 1.3 76.4 - - - +
408A PHE* 1.3 63.9 - - + +
410A GLU* 3.0 20.1 + - - +
411A ILE* 3.1 18.5 + - + +
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Residues in contact with PHE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ALA* 3.4 40.2 - - + -
309A THR* 4.3 7.6 - - + -
310A ALA* 4.3 0.4 - - + -
404A MET* 2.9 42.0 + - + -
405A GLY* 3.2 11.4 + - - +
407A VAL* 1.3 76.2 - - + +
409A TRP* 1.3 57.5 + - - +
411A ILE* 3.2 11.2 + - + +
412A ALA* 2.9 30.3 + - - +
467A MET* 3.8 24.9 - - + +
470A ILE* 3.8 22.0 - - + -
471A MET* 3.7 12.3 - - + +
474A CYS* 5.8 0.2 - - - -
488A ILE* 3.7 19.5 - - + -
492A LEU* 3.7 21.5 - - + -
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Residues in contact with TRP 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLY 3.1 11.2 + - - +
406A LEU* 3.3 9.2 - - - +
408A PHE* 1.3 76.9 - - - +
410A GLU* 1.3 82.9 + - + +
412A ALA 3.4 1.0 + - - -
413A ARG* 3.2 61.8 + - + +
425A GLN* 3.4 22.4 - - + -
426A LEU 3.6 9.2 - - - -
427A PRO* 3.6 24.9 - - + -
428A TYR 4.9 0.4 - - - -
429A TYR* 3.9 17.9 - + - -
430A ASP* 5.9 0.2 - - - -
452A PRO* 3.4 26.7 - - + +
453A ASN* 2.8 30.9 + - + -
454A ILE* 4.8 0.7 - - + -
455A PRO* 4.9 0.2 - - - +
458A TRP* 3.5 24.4 - + - -
471A MET* 3.7 13.6 - - - +
475A TRP* 3.9 16.8 - + + -
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 3.8 13.0 - - + +
336A SER* 2.7 23.7 + - - -
378A TYR* 2.6 35.5 + - - -
406A LEU 3.2 8.9 + - - +
407A VAL* 3.0 18.2 + - - +
409A TRP* 1.3 82.4 - - + +
411A ILE* 1.3 63.3 + - - +
413A ARG* 3.7 8.6 + - - +
414A ARG* 3.6 18.5 - - - +
424A TYR* 2.7 30.6 + - + -
425A GLN 3.8 11.7 - - - +
427A PRO* 3.6 18.6 - - + +
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.0 22.9 - - + -
292A LEU* 3.9 20.6 - - + -
297A VAL* 4.3 4.4 - - + +
302A MET* 3.9 27.6 - - + +
305A LEU* 4.0 38.8 - - + +
306A ALA* 4.2 16.2 - - + +
309A THR* 5.0 0.9 - - - +
407A VAL* 3.1 20.3 + - + +
408A PHE* 3.2 14.6 + - + +
410A GLU* 1.3 73.7 - - - +
412A ALA* 1.3 66.3 + - - +
414A ARG* 3.0 17.3 + - - +
415A CYS* 3.4 7.3 + - - +
467A MET* 4.9 1.8 - - + -
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A MET* 3.9 17.0 - - - -
408A PHE 2.9 16.5 + - - +
411A ILE* 1.3 75.5 - - - +
413A ARG* 1.4 62.0 + - - +
415A CYS* 2.9 18.7 + - - +
457A ARG* 3.5 8.7 + - - -
458A TRP* 3.6 27.0 + - + -
464A LEU* 3.9 18.2 - - + +
467A MET* 4.7 2.0 - - + -
471A MET* 3.8 11.7 - - + -
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TRP* 3.2 55.8 + - + +
410A GLU* 3.7 9.4 - - - +
411A ILE 3.2 0.2 - - - -
412A ALA* 1.4 75.7 - - - +
414A ARG* 1.3 61.8 + - + +
415A CYS 3.6 0.5 + - - -
421A HIS* 3.7 0.5 - - - +
422A GLU* 2.8 66.1 + - + +
423A ASP* 2.9 47.9 + - - +
424A TYR* 5.6 0.7 - - - -
425A GLN* 3.4 26.3 - - - +
429A TYR* 4.1 15.2 + - - -
453A ASN 5.4 0.8 + - - -
455A PRO* 5.3 5.3 - - - +
457A ARG* 3.6 1.9 + - - -
458A TRP* 3.5 13.9 - - + -
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 2.7 46.6 + - + +
293A ASN 3.6 13.1 + - - -
294A ARG 4.5 1.2 + - - -
295A TYR* 3.2 29.3 + - - +
296A THR* 3.4 18.6 - - - +
297A VAL* 2.9 28.0 + - + +
410A GLU 3.6 14.6 - - - +
411A ILE 3.0 9.8 + - - +
413A ARG* 1.3 76.1 - - - +
415A CYS* 1.3 60.1 + - - +
416A SER 3.2 1.9 + - - -
421A HIS* 3.7 17.8 + - - -
422A GLU 3.1 23.7 + - - -
423A ASP* 3.6 4.8 - - - +
424A TYR* 3.5 30.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il